TypeError while running Cell Types notebook from AllenSDK

Question

I am running the first lines of the cell types notebook:

sweep_number = 30
sweep_data = data_set.get_sweep(sweep_number)

And I get this error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-8-1ff88b13fc24> in <module>()
      4 
      5 sweep_number = 30
----> 6 sweep_data = data_set.get_sweep(sweep_number)
      7 

C:\ProgramData\Anaconda3\lib\site-packages\allensdk\core\nwb_data_set.py in get_sweep(self, sweep_number)
    112                 unit = stimulus_dataset.attrs["unit"]
    113                 unit_str = None
--> 114                 if unit.startswith('A'):
    115                     unit_str = "Amps"
    116                 elif unit.startswith('V'):

TypeError: startswith first arg must be bytes or a tuple of bytes, not str

Answer 1

The error you see is caused by the fact that the unit variable is a bytes literal and allensdk is trying to call endswith using a string on it. This cannot work, but that is not your fault. This is a common error when migrating from Python 2 to Python 3 (which introduced the bytes type; for detail see here). I would guess that you are running Python 3 and that causes the error, since allensdk cannot work with bytes here.

To work around this you either have to install Python 2, since you are using conda, create an environment that uses Python 2. This can be done as follows:

> conda create -n py2allen python=2.7
> activate py2allen
(py2allen)> pip install allensdk
(py2allen)> jupyter notebook

More information can be found here. If some of the requirements are not found, you can try to install them manually.